Large scale online environments, in which there are hundreds of thousands, and often millions of links, present an emerging phenomenon where millions of people come together online to share and consume information. The resulting massive amounts of data have been a fertile ground for quantitative researchers. Qualitative studies of these environments are less common, suggesting that the scale and the constant change of these environments pose considerable challenges for qualitative researchers. We present an exploratory study into the challenges and opportunities experienced by researchers conducting qualitative research in large scale online environments, and a meta-analysis of papers from the ACM Digital Library that reveals how few published research studies use qualitative methods to investigate large-scale online environments. We discuss practical and theoretical issues arising from the unique stance of qualitative researchers in these environments.